Advanced biology course, or willingness to read up on such topics extensively.

Material Availability

A computer with Internet access is necessary for this project.

Cost

Very Low (under $20)

Safety

No issues

*Note: This is an abbreviated Project Idea, without notes to start your background research, a specific list of materials, or a procedure for how to do the experiment. You can identify abbreviated Project Ideas by the asterisk at the end of the title. If you want a Project Idea with full instructions, please pick one without an asterisk.

Abstract

Some sequences of RNA can catalyze biochemical reactions, much like protein enzymes. These catalytic RNA sequences are called ribozymes. The function of a ribozyme depends upon the primary sequence of the RNA which folds into a 3-D structure. How do different ribozyme sequences fold? You can search for ribozyme sequences using Entrez BLAST (NCBI, 2006). Then you can use a program like MFOLD (http://bioweb.pasteur.fr/seqanal/interfaces/mfold-simple.html) to submit your sequence for an analysis of its predicted 3-D structures based upon thermodynamics (Zuker, 2006; Zuker, 2003). Compare the different predicted structures and see if they are similar or different. If possible, compare the predicted structures to a published crystal structure. How close was the predicted structure to the crystal structure? Can you identify primary sequence elements in your molecule that contribute to parts of the structure? For example, palindromic stretches can form stem-loop structures. You can also mutate the sequence and submit the new sequence to MFOLD. How does this alter the 3-D structure? Can you use this computational method to identify potentially important nucleotides?

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